[English] 日本語
Yorodumi
- PDB-2qjy: Crystal structure of rhodobacter sphaeroides double mutant with s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qjy
TitleCrystal structure of rhodobacter sphaeroides double mutant with stigmatellin and UQ2
Components
  • Cytochrome b
  • Cytochrome c1
  • Ubiquinol-cytochrome c reductase iron-sulfur subunit
KeywordsOXIDOREDUCTASE / Cytochrome B / 8 TM helixces Cytochrome C1 / 1 c-term TM helix Rieske / 1 N-term TM helix
Function / homology
Function and homology information


respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / heme binding / metal ion binding / membrane / plasma membrane
Similarity search - Function
Ubiquitinol-cytochrome C reductase, Fe-S subunit, TAT signal / Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal / Single helix bin / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal ...Ubiquitinol-cytochrome C reductase, Fe-S subunit, TAT signal / Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal / Single helix bin / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Cytochrome b / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / : / Cytochrome c1 / Cytochrome C1 family / : / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Rieske iron-sulphur protein / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / Chem-LOP / STIGMATELLIN A / STRONTIUM ION / UBIQUINONE-2 / Cytochrome c1 / Cytochrome b / Ubiquinol-cytochrome c reductase iron-sulfur subunit / Cytochrome c1
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsEsser, L. / Xia, D.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Inhibitor-complexed Structures of the Cytochrome bc1 from the Photosynthetic Bacterium Rhodobacter sphaeroides.
Authors: Esser, L. / Elberry, M. / Zhou, F. / Yu, C.A. / Yu, L. / Xia, D.
History
DepositionJul 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome b
B: Cytochrome c1
C: Ubiquinol-cytochrome c reductase iron-sulfur subunit
D: Cytochrome b
E: Cytochrome c1
F: Ubiquinol-cytochrome c reductase iron-sulfur subunit
G: Cytochrome b
H: Cytochrome c1
I: Ubiquinol-cytochrome c reductase iron-sulfur subunit
J: Cytochrome b
K: Cytochrome c1
L: Ubiquinol-cytochrome c reductase iron-sulfur subunit
M: Cytochrome b
N: Cytochrome c1
O: Ubiquinol-cytochrome c reductase iron-sulfur subunit
P: Cytochrome b
Q: Cytochrome c1
R: Ubiquinol-cytochrome c reductase iron-sulfur subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)620,44578
Polymers596,68718
Non-polymers23,75860
Water12,574698
1
A: Cytochrome b
B: Cytochrome c1
C: Ubiquinol-cytochrome c reductase iron-sulfur subunit
D: Cytochrome b
E: Cytochrome c1
F: Ubiquinol-cytochrome c reductase iron-sulfur subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,78425
Polymers198,8966
Non-polymers7,88819
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35820 Å2
ΔGint-432 kcal/mol
Surface area69660 Å2
MethodPISA, PQS
2
G: Cytochrome b
H: Cytochrome c1
I: Ubiquinol-cytochrome c reductase iron-sulfur subunit
J: Cytochrome b
K: Cytochrome c1
L: Ubiquinol-cytochrome c reductase iron-sulfur subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,81926
Polymers198,8966
Non-polymers7,92420
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35780 Å2
ΔGint-441 kcal/mol
Surface area69930 Å2
MethodPISA, PQS
3
M: Cytochrome b
N: Cytochrome c1
O: Ubiquinol-cytochrome c reductase iron-sulfur subunit
P: Cytochrome b
Q: Cytochrome c1
R: Ubiquinol-cytochrome c reductase iron-sulfur subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,84227
Polymers198,8966
Non-polymers7,94621
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35830 Å2
ΔGint-441 kcal/mol
Surface area69690 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)351.891, 147.042, 161.312
Angle α, β, γ (deg.)90.00, 104.25, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 3 types, 18 molecules ADGJMPBEHKNQCFILOR

#1: Protein
Cytochrome b


Mass: 50157.539 Da / Num. of mol.: 6 / Mutation: S287R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: petB, fbcB / Plasmid: pRKD418 / Production host: Escherichia coli (E. coli) / References: UniProt: Q02761
#2: Protein
Cytochrome c1


Mass: 29373.953 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: fbcC / Plasmid: pRKD418 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3IY11, UniProt: Q02760*PLUS
#3: Protein
Ubiquinol-cytochrome c reductase iron-sulfur subunit / Rieske iron-sulfur protein / RISP


Mass: 19916.322 Da / Num. of mol.: 6 / Mutation: V135S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: petA, fbcF / Plasmid: pRKD418 / Production host: Escherichia coli (E. coli) / Strain (production host): pRKD418 / References: UniProt: Q02762, quinol-cytochrome-c reductase

-
Sugars , 1 types, 6 molecules

#9: Sugar
ChemComp-BGL / 2-O-octyl-beta-D-glucopyranose / 2-O-octyl-beta-D-glucose / 2-O-octyl-D-glucose / 2-O-octyl-glucose


Type: D-saccharide, beta linking / Mass: 292.369 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-D-Glcp2octylIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

-
Non-polymers , 9 types, 752 molecules

#4: Chemical
ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Sr
#5: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#6: Chemical
ChemComp-SMA / STIGMATELLIN A


Mass: 514.650 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C30H42O7
#7: Chemical
ChemComp-LOP / (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE / LAURYL OLEYL PHOSPHATIDYL ETHANOLAMINE


Mass: 661.890 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C35H68NO8P / Comment: phospholipid*YM
#8: Chemical
ChemComp-UQ2 / UBIQUINONE-2


Mass: 318.407 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C19H26O4
#10: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe2S2
#11: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#12: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 698 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.39 Å3/Da / Density % sol: 63.69 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 50 mM BisTris 7.2pH, 0.5% beta-octylglucoside, 0.1% sucrose mono caprate, 7% PEG400, 5-10 mM Sr nitrate, 105 Glycerol, 200 mM NaCl, 5 mM NaN3, VAPOR DIFFUSION, SITTING DROP, temperature 288K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.75 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 10, 2006 / Details: mirrors
RadiationMonochromator: silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.75 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 295863 / Num. obs: 293559 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 / Redundancy: 5 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.107 / Rsym value: 0.107 / Net I/σ(I): 14.32
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 1.25 / Num. unique all: 23288 / Rsym value: 0.577 / % possible all: 74.7

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FYN

2fyn


Resolution: 2.4→18 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 6986056.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Complex NCS restraints (89)
RfactorNum. reflection% reflectionSelection details
Rfree0.251 4924 1.7 %SHELLS
Rwork0.226 ---
all0.237 290327 --
obs0.226 290127 93.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.972 Å2 / ksol: 0.341076 e/Å3
Displacement parametersBiso mean: 70.1 Å2
Baniso -1Baniso -2Baniso -3
1--7.67 Å20 Å2-13.83 Å2
2---7.17 Å20 Å2
3---14.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 2.4→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms40398 0 1560 698 42656
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.68
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d1.11
X-RAY DIFFRACTIONc_mcbond_it1.971.5
X-RAY DIFFRACTIONc_mcangle_it3.162
X-RAY DIFFRACTIONc_scbond_it2.92
X-RAY DIFFRACTIONc_scangle_it4.092.5
Refine LS restraints NCSNCS model details: RESTRAINED
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.344 613 1.5 %
Rwork0.344 39198 -
obs--77.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep_MET.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3Ligand.parLigand.top
X-RAY DIFFRACTION4cis_peptide.paramwater.top
X-RAY DIFFRACTION5water_rep.param

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more